SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

As a conceptual model of disease mechanisms, a disease map integrates available knowledge and is applied for data interpretation, predictions and hypothesis generation. It is possible to model disease mechanisms on different levels of granularity and adjust the approach to the goals of a particular project. This rich environment together with requirements for high-quality network reconstruction makes it challenging for new curators and groups to be quickly introduced to the development methods. In this review, we offer a step-by-step guide for developing a disease map within its mainstream pipeline that involves using the CellDesigner tool for creating and editing diagrams and the MINERVA Platform for online visualisation and exploration. We also describe how the Neo4j graph database environment can be used for managing and querying efficiently such a resource. For assessing the interoperability and reproducibility we apply FAIR principles.

StonPy: a tool to parse and query collections of SBGN maps in a graph database

SUMMARY

The systems biology graphical notation (SBGN) has become the de facto standard for the graphical representation of molecular maps. Having rapid and easy access to the content of large collections of maps is necessary to perform semantic or graph-based analysis of these resources. To this end, we propose StonPy, a new tool to store and query SBGN maps in a Neo4j graph database. StonPy notably includes a data model that takes into account all three SBGN languages and a completion module to automatically build valid SBGN maps from query results. StonPy is built as a library that can be integrated into other software and offers a command-line interface that allows users to easily perform all operations.

AVAILABILITY AND IMPLEMENTATION

StonPy is implemented in Python 3 under a GPLv3 license. Its code and complete documentation are freely available from https://github.com/adrienrougny/stonpy.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Design considerations for representing systems biology information with the Systems Biology Graphical Notation

Visual representations are commonly used to explore, analyse, and communicate information and knowledge in systems biology and beyond. Such visualisations not only need to be accurate but should also be aesthetically pleasing and informative. Using the example of the Systems Biology Graphical Notation (SBGN) we will investigate design considerations for graphically presenting information from systems biology, in particular regarding the use of glyphs for types of information, the style of graph layout for network representation, and the concept of bricks for visual network creation.